qHTSWaterfall-vignette

library(qHTSWaterfall)

#############
# Use this method to start the user interface Shiny Application
#############

# This will allow one to use the user interface and sample data or user input data
# qHTSWaterfall::runQHTSWaterfallApp()


#############
# Use the code below to use R scripting to produce the Waterfall Plot
#############

# Specify a comma separateed input file. In this example, one is included as 
# part of the qHTSPackage. If using your own file, provide the file path here.

# This example features active compounds from this study:
# Martinez NJ, Braisted JC, Dranchak PK, Moran JJ, Larson H, Queme B, Pak E, Dutra A, Rai G, 
# Cheng KC, Svaren J, Inglese J. Genome-Edited Coincidence and PMP22-HiBiT Fusion Reporter Cell 
# Lines Enable an Artifact-Suppressive Quantitative High-Throughput Screening Strategy for PMP22
# Gene-Dosage Disorder Drug Discovery. ACS Pharmacol Transl Sci. 2021 Jun 10;4(4):1422-1436.
# doi: 10.1021/acsptsci.1c00110. PMID: 34423274; PMCID: PMC8369676.


inputFile <- system.file("extdata", "NCATS_CMT1A_PMP22_Follow_Up.csv", package="qHTSWaterfall")

# Non-PubChemm input requires a list of log-molar concentrations, from low to high #concentration.
logConc <- c(
-9.011761791,
-8.534640544,
-8.057519287,
-7.580398031,
-7.103276777,
-6.626155522,
-6.149034267,
-5.671913012,
-5.194791758,
-4.717670503,
-4.240549248
)

# the main method call with parameters. Use 'help(plotWaterfall' for parameter descriptions.)
# Note: The displayed resulting plot shown in this vignette page is a low resolution static image.
# The method will return a high resolution 3D rendering (from the rgl package) that can be resized
# and rotated.
responseAxisConfig = list(min=-115, max=50, tickSizeVal=25, firstTick=-100)
concAxisConfig = list(min=-9.2, max=-3.9, tickSizeVal=1.0, firstTick=-4)
planeColors = list(basePlaneColor="#b8b6b6", rightPlaneColor="#999494", leftPlaneColor="#6e6868")

qHTSWaterfall::plotWaterfall(
  inputFile,
  activityReadouts = c("nluc","fluc"),
  pointColors = c("royalblue3", "darkgreen"),
  curveColors = c("royalblue3", "darkgreen"),
  inactiveColor = "gray",
  pointSize = 1.0,
  alpha = 1,
  plotInactivePoints = F,
  curveResolution = 250,
  plotAspectRatio = c(1.5,1,3),
  lineWeight = 1.5,
  fileFormat = 'ncats_qhts',
  planeColors = planeColors,
  showCurveNumberLabels = T,
  concAxisConfig = concAxisConfig,
  responseAxisConfig = responseAxisConfig
)
#> [1] "starting plotWaterfall method.."